1H1R

Structure of human Thr160-phospho CDK2/cyclin A complexed with the inhibitor NU6086


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-Based Design of a Potent Purine-Based Cyclin-Dependent Kinase Inhibitor

Davies, T.G.Bentley, J.Arris, C.E.Boyle, F.T.Curtin, N.J.Endicott, J.A.Gibson, A.E.Golding, B.T.Griffin, R.J.Hardcastle, I.R.Jewsbury, P.Johnson, L.N.Mesguiche, V.Newell, D.R.Noble, M.E.M.Tucker, J.A.Wang, L.Whitfield, H.J.

(2002) Nat.Struct.Mol.Biol. 9: 745

  • DOI: 10.1038/nsb842
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aberrant control of cyclin-dependent kinases (CDKs) is a central feature of the molecular pathology of cancer. Iterative structure-based design was used to optimize the ATP- competitive inhibition of CDK1 and CDK2 by O(6)-cyclohexylmethylguanines, re ...

    Aberrant control of cyclin-dependent kinases (CDKs) is a central feature of the molecular pathology of cancer. Iterative structure-based design was used to optimize the ATP- competitive inhibition of CDK1 and CDK2 by O(6)-cyclohexylmethylguanines, resulting in O(6)-cyclohexylmethyl-2-(4'- sulfamoylanilino)purine. The new inhibitor is 1,000-fold more potent than the parent compound (K(i) values for CDK1 = 9 nM and CDK2 = 6 nM versus 5,000 nM and 12,000 nM, respectively, for O(6)-cyclohexylmethylguanine). The increased potency arises primarily from the formation of two additional hydrogen bonds between the inhibitor and Asp 86 of CDK2, which facilitate optimum hydrophobic packing of the anilino group with the specificity surface of CDK2. Cellular studies with O(6)-cyclohexylmethyl-2-(4'- sulfamoylanilino) purine demonstrated inhibition of MCF-7 cell growth and target protein phosphorylation, consistent with CDK1 and CDK2 inhibition. The work represents the first successful iterative synthesis of a potent CDK inhibitor based on the structure of fully activated CDK2-cyclin A. Furthermore, the potency of O(6)-cyclohexylmethyl-2-(4'- sulfamoylanilino)purine was both predicted and fully rationalized on the basis of protein-ligand interactions.


    Organizational Affiliation

    Laboratory of Molecular Biophysics and Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CELL DIVISION PROTEIN KINASE 2
A, C
303Homo sapiensMutation(s): 0 
Gene Names: CDK2 (CDKN2)
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to Gene View: CDK2
Go to UniProtKB:  P24941
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYCLIN A2
B, D
258Homo sapiensMutation(s): 0 
Gene Names: CCNA2 (CCN1, CCNA)
Find proteins for P20248 (Homo sapiens)
Go to Gene View: CCNA2
Go to UniProtKB:  P20248
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6CP
Query on 6CP

Download SDF File 
Download CCD File 
A, C
6-CYCLOHEXYLMETHOXY-2-(3'-CHLOROANILINO) PURINE
C18 H20 Cl N5 O
OUEGMEMDEAOAEG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, C
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6CPIC50: 2300 nM BINDINGMOAD
6CPIC50: 2300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.110α = 90.00
b = 134.950β = 90.00
c = 148.330γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-09-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance